sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2007-09-16
| Name: | Riboflavin kinase |
|---|---|
| ID: | RIFK_METJA |
| AC: | Q60365 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | 2.7.1.161 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 36.197 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | CDP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.964 | 371.250 |
| % Hydrophobic | % Polar |
|---|---|
| 65.45 | 34.55 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 73.78 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -14.8165 | -15.4736 | -2.774 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C5' | CB | GLU- 17 | 3.31 | 0 | Hydrophobic |
| O3P | N | GLY- 18 | 3.01 | 120.21 | H-Bond (Protein Donor) |
| C6 | CB | PHE- 21 | 3.63 | 0 | Hydrophobic |
| C9A | CB | PHE- 21 | 3.98 | 0 | Hydrophobic |
| C2' | CE2 | PHE- 21 | 3.72 | 0 | Hydrophobic |
| C7M | CG | LEU- 22 | 4.36 | 0 | Hydrophobic |
| C8M | CD1 | LEU- 22 | 4.2 | 0 | Hydrophobic |
| C7M | CD1 | TYR- 27 | 4.28 | 0 | Hydrophobic |
| C7M | CE2 | PHE- 31 | 3.8 | 0 | Hydrophobic |
| C8M | CG2 | THR- 43 | 3.4 | 0 | Hydrophobic |
| O1P | ND2 | ASN- 45 | 3.29 | 136.97 | H-Bond (Protein Donor) |
| O2P | ND2 | ASN- 45 | 3.41 | 162.8 | H-Bond (Protein Donor) |
| O4 | N | PHE- 73 | 3.32 | 133.87 | H-Bond (Protein Donor) |
| C6 | CG1 | VAL- 75 | 3.54 | 0 | Hydrophobic |
| C8M | CG2 | VAL- 94 | 3.72 | 0 | Hydrophobic |
| C1' | CG | PRO- 96 | 3.68 | 0 | Hydrophobic |
| C9 | CG | PRO- 96 | 3.33 | 0 | Hydrophobic |
| C1' | CB | THR- 99 | 4.38 | 0 | Hydrophobic |
| O3' | OG1 | THR- 99 | 3.06 | 141.26 | H-Bond (Protein Donor) |
| O4' | OG1 | THR- 99 | 3.4 | 146.62 | H-Bond (Protein Donor) |
| C3' | CD2 | TYR- 100 | 3.69 | 0 | Hydrophobic |
| C4' | CE2 | TYR- 100 | 3.77 | 0 | Hydrophobic |
| O3' | N | TYR- 100 | 2.92 | 149.14 | H-Bond (Protein Donor) |
| O2P | OH | TYR- 100 | 2.71 | 131 | H-Bond (Protein Donor) |
| O4' | OE1 | GLU- 107 | 3.24 | 141.3 | H-Bond (Ligand Donor) |
| O1P | MG | MG- 1136 | 2.01 | 0 | Metal Acceptor |
